The karstic Zrmanja River discharges into the eastern Adriatic Sea, forming a highly stratified estuary with a sharp halocline that divides upper brackish and lower marine layers. Low orthophosphate concentrations and high Redfield ratios indicate that phosphorus limits phytoplankton growth. In addition, high transparency (avg 6.7 m) and oxygen saturation (avg 98.78%) indicate oligotrophy. Maximum phytoplankton abundance reached 3.4 × 106 cells·l-1 in early spring, a period when the community was composed mainly of diatoms. Dinoflagellates and nanoplanktonic phytoplankton dominated in summer; coccolithophorids and silicoflagellates characterized autumn. Stable conditions in the middle and lower estuary provided a suitable setting for development of microphytoplanktonic diatoms, whereas unstable conditions (frequent salinity variations) at the head of the estuary favored nanophytoplankton. Canonical correspondence analysis identified salinity, temperature, and river inflow as the main factors influencing phytoplankton development. Nutrients strongly limited phytoplankton growth in summer when the river discharge was a minimum.